Hi there.
Looking at what you've said it sounds like she likes a really short first A time but is then taking an UT short nap. I agree with Weaver's advice regarding extending A times but would also say if you are totally convinced from your trials that she can only handle a 1hr first A then a short nap, then perhaps this just suits her, LOs are all individual after all. If this is the case you could try out a sort of flipped EASY where the CN comes at the beginning of the day and longer naps later, basically just accepting that first A time and nap as both short and working a longer A and nap time thereafter for the rest of the day.
It seems to me you are spending a long time trying to settle her and in some instances (like nap 2) the A is short but you are then spending a huge amount of time (and energy) into keeping her asleep or resettling. I would really look at keeping her up longer for that A and ensure she really is super tired before the nap - as you are putting in so much work already it wouldn't really be anything additional if you were to go in at the 20 min mark and shush/pat her through for 10 or 20 mins with a W2S to help her learn to stay asleep. I actually did this with my DS when he was older and dropping to 1 nap, I went in every 19 mins to help him through the transition until he was able to do it alone. I was literally only in the room 2 mins because I timed it right up to the mark of the minimum help needed and it avoided a lot of crying and a lot of trying to resettle once he was fully awake. It can work wonders for younger babies learning to get into a healthier sleep routine too.
So, the other thing I noticed was here:
3:50-4:15 - try to put her back to sleep
4:15 - take downstairs and try to not feed her till the 3 hour mark
5 - feed
5:45 - try to put down for nap
6-6:30 - sleep
She is awake 2hrs 10 mins. You say yourself she cannot handle an A time this long, you might not even have noticed that the A times are getting so long later in the day. My feeling is that you started WD for nap too early, at just 1 hr and this was after a 1.5hr nap too, so she was UT for the nap and fought it. UT babies sometimes go to sleep because they are not used to staying awake longer, it has become their habit to be tired at a short A time, but unfortunately they then only sleep a short nap and take a lot of work to get back to sleep (if ever they go back to sleep) and can be very cranky due to having had the short A and short nap. In fact the waking screaming at 39-45 mins as you describe in your first post, is exactly what my LO did when put down UT.
I would track your A, E and S time in separate columns on paper if possible and note down her A time from eyes open, add 1hr 30 A and note down when her next nap is due. After a short nap I would not decrease the A by much at all (if any) max 10 mins.
I'd also try her on a much shorter WD, have you ever tried that? Some like a good 20 min WD as described in the BW books, for others this drives them insane, mine liked roughly 3 mins. It might be worth a shot.
When Tracy was getting a LO into a suitable routine she used (almost) set times for a couple of days, this meant LOs had some super long A times if they woke early from a nap and refused to resettle as they were not invited for their next nap until the 'set' time (Tracy describes do anything needed to keep baby awake, a fan dance if necessary). I know you have a 3yo to care for at the same time but it does sound to me like this routine might be less work for you rather than more.
A few things for you to think about